Detection of nucleic acids in a sample is useful in diagnostic, therapeutic, forensic, agricultural, food science applications and other areas. One technique for purifying a target polynucleotide, which is often used in diagnostic procedures, involves capturing a target nucleic acid onto a solid support. The solid support retains the target nucleic acid during one or more washing steps of the target nucleic acid purification procedure. The captured target nucleic acid sequence can be analyzed by various methods. One such method uses nucleic acid probes that hybridize to a target sequence. Probes can be designed to detect different target sequences such as those characteristic of microorganisms, viruses, human genes, plant or animal genes, and/or pathogenic conditions. Additional analysis techniques that benefit from captured target nucleic acids include amplification assays, microarrays, sequencing assays, mass spectrometry of nucleic acids.
A target nucleic acid can be captured using a target capture oligomer that hybridizes to bind both to a target nucleic acid and to a nucleic acid fixed to a solid support. The target capture oligomer joins the target nucleic acid to the solid support to produce a complex comprising a bound target nucleic acid. A labeled probe can be hybridized to the bound target and unbound labeled probe can be washed away from the solid support (see Stabinsky, U.S. Pat. No. 4,751,177).
A variation of a target capture oligomer has been described in which in the absence of target the capture probe exists as a stem-loop structure and in the presence of a target nucleic acid, the target nucleic acid binds to the loop portion, opening up the stem and making one of the arms of the loop accessible to bind an immobilized probe (see US 20060068417). Such an arrangement can be useful in reducing the ability of a target capture oligomer to hybridize with an immobilized probe before the target capture oligomer has bound to its target nucleic acid.